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MIXS_yaml:agriculture from microbiomedata/mixs/main/model/schema/mixs.yaml is not a valid URI or CURIE #1367

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turbomam opened this issue Nov 17, 2023 · 7 comments
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MIXS_yaml:agriculture from microbiomedata/mixs/main/model/schema/mixs.yaml is not a valid URI or CURIE #1367

turbomam opened this issue Nov 17, 2023 · 7 comments
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turbomam commented Nov 17, 2023 •
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In https://github.com/microbiomedata/nmdc-schema/tree/1364-limit-linkml-and-runtime-to-161

with linkml and linkml-runtime 1.6.1 (which is still behind 1.6.2 for both!)

poetry run do_shuttle \
	--recipient_model assets/other_mixs_yaml_files/mixs_template.yaml \
	--config_tsv local/mixs_regen/import_slots_regardless_gen.tsv \
	--yaml_output local/mixs_regen/mixs_subset.yaml

see

Traceback (most recent call last):
File "/home/runner/.cache/pypoetry/virtualenvs/nmdc-schema-eC8G10po-py3.9/bin/do_shuttle", line 8, in
sys.exit(do_shuttle())
File "/home/runner/.cache/pypoetry/virtualenvs/nmdc-schema-eC8G10po-py3.9/lib/python3.9/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/runner/.cache/pypoetry/virtualenvs/nmdc-schema-eC8G10po-py3.9/lib/python3.9/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/runner/.cache/pypoetry/virtualenvs/nmdc-schema-eC8G10po-py3.9/lib/python3.9/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/runner/.cache/pypoetry/virtualenvs/nmdc-schema-eC8G10po-py3.9/lib/python3.9/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/home/runner/.cache/pypoetry/virtualenvs/nmdc-schema-eC8G10po-py3.9/lib/python3.9/site-packages/sheets_and_friends/shuttle.py", line 44, in do_shuttle
shuttle.prep_views_dict()
File "/home/runner/.cache/pypoetry/virtualenvs/nmdc-schema-eC8G10po-py3.9/lib/python3.9/site-packages/sheets_and_friends/shuttle.py", line 97, in prep_views_dict
temp = SchemaView(k)
File "/home/runner/.cache/pypoetry/virtualenvs/nmdc-schema-eC8G10po-py3.9/lib/python3.9/site-packages/linkml_runtime/utils/schemaview.py", line 138, in init
schema = load_schema_wrap(schema)
File "/home/runner/.cache/pypoetry/virtualenvs/nmdc-schema-eC8G10po-py3.9/lib/python3.9/site-packages/linkml_runtime/utils/schemaview.py", line 70, in load_schema_wrap
schema = yaml_loader.load(path, target_class=SchemaDefinition, **kwargs)
File "/home/runner/.cache/pypoetry/virtualenvs/nmdc-schema-eC8G10po-py3.9/lib/python3.9/site-packages/linkml_runtime/loaders/loader_root.py", line 71, in load
results = self.load_any(*args, **kwargs)
File "/home/runner/.cache/pypoetry/virtualenvs/nmdc-schema-eC8G10po-py3.9/lib/python3.9/site-packages/linkml_runtime/loaders/yaml_loader.py", line 41, in load_any
return self._construct_target_class(data_as_dict, target_class)
File "/home/runner/.cache/pypoetry/virtualenvs/nmdc-schema-eC8G10po-py3.9/lib/python3.9/site-packages/linkml_runtime/loaders/loader_root.py", line 132, in _construct_target_class
return target_class(**data_as_dict)
File "", line 66, in init
File "/home/runner/.cache/pypoetry/virtualenvs/nmdc-schema-eC8G10po-py3.9/lib/python3.9/site-packages/linkml_runtime/linkml_model/meta.py", line 564, in post_init
self.imports = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.imports]
File "/home/runner/.cache/pypoetry/virtualenvs/nmdc-schema-eC8G10po-py3.9/lib/python3.9/site-packages/linkml_runtime/linkml_model/meta.py", line 564, in
self.imports = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.imports]
File "/home/runner/.cache/pypoetry/virtualenvs/nmdc-schema-eC8G10po-py3.9/lib/python3.9/site-packages/linkml_runtime/utils/metamodelcore.py", line 104, in init
raise ValueError(f"{v} is not a valid URI or CURIE")
ValueError: MIXS_yaml:agriculture is not a valid URI or CURIE
make: *** [project.Makefile:85: local/mixs_regen/mixs_subset.yaml] Error 1
@turbomam turbomam self-assigned this Nov 17, 2023
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looks like it will work under 1.6.0/1.6.0

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see also

@turbomam
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now getting

poetry run gen-project \
        --exclude excel \
        --exclude graphql \
        --exclude jsonld \
        --exclude markdown \
        --exclude proto \
        --exclude shacl \
        --exclude shex \
        --exclude sqlddl \
        --include jsonldcontext \
        --include jsonschema \
        --include owl \
        --include python \
        --include rdf \
        -d project src/schema/nmdc.yaml && mv project/*.py nmdc_schema

Traceback (most recent call last):
File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/bin/gen-project", line 8, in
sys.exit(cli())
File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml/generators/projectgen.py", line 253, in cli
gen.generate(yamlfile, project_config)
File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml/generators/projectgen.py", line 153, in generate
gen_dump = gen.serialize(**serialize_args)
File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml/generators/owlgen.py", line 192, in serialize
self.as_graph()
File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml/generators/owlgen.py", line 178, in as_graph
self.add_class(cls)
File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml/generators/owlgen.py", line 314, in add_class
superclass_expr = self.transform_class_expression(cls)
File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml/generators/owlgen.py", line 372, in transform_class_expression
x = self.transform_class_slot_expression(cls, slot, slot)
File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml/generators/owlgen.py", line 480, in transform_class_slot_expression
owl_exprs.append(self._class_uri(ClassDefinitionName(range)))
File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml/generators/owlgen.py", line 843, in _class_uri
return URIRef(self.schemaview.get_uri(c, expand=True, native=self.use_native_uris))
File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml_runtime/utils/schemaview.py", line 916, in get_uri
e_name = e.name
AttributeError: 'NoneType' object has no attribute 'name'

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turbomam commented Nov 17, 2023 •
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rebuilding environment from main branch's poetry.lock file

-> 1.6.1/1.6.0

make squeaky-clean all test completed

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[tool.poetry.dependencies]
linkml = ">=1.5.0, <1.6.2"
linkml-runtime = ">=1.5.0, <1.6.1"
poetry update linkml

Updating dependencies
Resolving dependencies... (5.1s)

No dependencies to install or update

Writing lock file

poetry update linkml-runtime

Updating dependencies
Resolving dependencies... (3.3s)

No dependencies to install or update

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introduced by https://raw.githubusercontent.com/microbiomedata/mixs/main/model/schema/mixs.yaml

@turbomam turbomam changed the title MIXS_yaml:agriculture is not a valid URI or CURIE MIXS_yaml:agriculture from microbiomedata/mixs/main/model/schema/mixs.yaml is not a valid URI or CURIE Nov 17, 2023
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turbomam commented Nov 17, 2023 •
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skipping tests from tests/test_nmdc_mixs_merged_view.py

should be resolved by updating to MIxS 6.2

see also

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